@molgenis/vip-report-template 6.1.1 → 7.0.0

package/src/mocks/GRCh37/sampleTree.json

@@ -0,0 +1,143 @@
+{
+  "rootNode": "gt",
+  "nodes": {
+    "GT": {
+      "label": "Genotype",
+      "description": "Genotype",
+      "type": "CATEGORICAL",
+      "field": "FORMAT/GENOTYPE/TYPE",
+      "outcomeMap": {
+        "HET": {
+          "nextNode": "gq"
+        },
+        "HOM_REF": {
+          "nextNode": "exit_u3"
+        },
+        "HOM_VAR": {
+          "nextNode": "gq"
+        },
+        "MIXED": {
+          "nextNode": "gq"
+        },
+        "NO_CALL": {
+          "nextNode": "exit_u3"
+        },
+        "UNAVAILABLE": {
+          "nextNode": "exit_u3"
+        }
+      },
+      "outcomeMissing": {
+        "nextNode": "gq"
+      },
+      "outcomeDefault": {
+        "nextNode": "gq"
+      }
+    },
+    "GQ": {
+      "label": "Genotype Quality",
+      "type": "BOOL",
+      "description": "Genotype quality",
+      "query": {
+        "field": "FORMAT/GQ",
+        "operator": ">=",
+        "value": 20
+      },
+      "outcomeTrue": {
+        "nextNode": "dp"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "dp"
+      }
+    },
+    "DP": {
+      "label": "Sequencing Depth",
+      "type": "BOOL",
+      "description": "Sequencing depth",
+      "query": {
+        "field": "FORMAT/DP",
+        "operator": ">=",
+        "value": 10
+      },
+      "outcomeTrue": {
+        "nextNode": "vim"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "vim"
+      }
+    },
+    "VIM": {
+      "label": "Inheritance",
+      "type": "BOOL",
+      "description": "Inheritance match",
+      "query": {
+        "field": "FORMAT/VIG",
+        "operator": "contains",
+        "value": "field:INFO/CSQ/Gene"
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u1"
+      },
+      "outcomeFalse": {
+        "nextNode": "vid"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u2"
+      }
+    },
+    "VID": {
+      "label": "Denovo",
+      "type": "BOOL",
+      "description": "Inheritance denovo",
+      "query": {
+        "field": "FORMAT/VID",
+        "operator": "==",
+        "value": 1
+      },
+      "outcomeTrue": {
+        "nextNode": "exit_u1"
+      },
+      "outcomeFalse": {
+        "nextNode": "exit_u3"
+      },
+      "outcomeMissing": {
+        "nextNode": "exit_u2"
+      }
+    },
+    "exit_u1": {
+      "label": "probably",
+      "description": "Usable: probably",
+      "type": "LEAF",
+      "class": "U1"
+    },
+    "exit_u2": {
+      "label": "maybe",
+      "description": "Usable: maybe",
+      "type": "LEAF",
+      "class": "U2"
+    },
+    "exit_u3": {
+      "label": "probably not",
+      "description": "Usable: probably not",
+      "type": "LEAF",
+      "class": "U3"
+    },
+    "exit_ok": {
+      "label": "Okey",
+      "description": "OK",
+      "type": "LEAF",
+      "class": "OK"
+    },
+    "exit_nok": {
+      "label": "Not Okey",
+      "description": "NOK",
+      "type": "LEAF",
+      "class": "NOK"
+    }
+  }
+}

package/src/mocks/GRCh37/static.ts

@@ -1,6 +1,9 @@
+/* eslint-disable */
+// @ts-nocheck
 import cramUrl from "./alignment.cram.blob";
 import craiUrl from "./alignment.cram.crai.blob";
 import decisionTreeJson from "./decisionTree.json";
+import sampleTreeJson from "./sampleTree.json";
 import fastaUrl1_10042288_10042788 from "./fasta/1-10042288-10042788.fasta.gz.blob";
 import fastaUrl1_16375333_16375833 from "./fasta/1-16375333-16375833.fasta.gz.blob";
 import fastaUrl1_16376162_16376662 from "./fasta/1-16376162-16376662.fasta.gz.blob";
@@ -39,75 +42,76 @@ import fastaUrlX_48932771_48933271 from "./fasta/X-48932771-48933271.fasta.gz.bl
 import fastaUrlY_2655391_2655891 from "./fasta/Y-2655391-2655891.fasta.gz.blob";
 import fastaUrlMT_15076_15576 from "./fasta/MT-15076-15576.fasta.gz.blob";
 import genesUrl from "./genes.gff.gz.blob";
-import vcfMetaJson from "./field_metadata.json";
 import vcfUrlFamily from "./vcf/family.vcf.blob";
-import vcfUrlNoVep from "./vcf/no_vep.vcf.blob";
-import vcfUrlSamples0 from "./vcf/samples_0.vcf.blob";
-import vcfUrlSamples1 from "./vcf/samples_1.vcf.blob";
-import vcfUrlSamples100 from "./vcf/samples_100.vcf.blob";
-
+/* eslint-enable */
+import vcfMetaJson from "./field_metadata.json";
 import { fetchAsBytes } from "../utils";
-import { DecisionTree } from "@molgenis/vip-report-api/src/Api";
-import { Metadata } from "@molgenis/vip-report-vcf/src/FieldMetadata";
-
-export const cram = await fetchAsBytes(cramUrl as string);
-export const crai = await fetchAsBytes(craiUrl as string);
-
-export const decisionTree: DecisionTree = decisionTreeJson as unknown as DecisionTree;
+import { DecisionTree } from "@molgenis/vip-report-api";
+import { SupplementaryMetadata } from "@molgenis/vip-report-vcf";
 
-export const fastaGz = {
-  "1:10042288-10042788": await fetchAsBytes(fastaUrl1_10042288_10042788 as string),
-  "1:16375333-16375833": await fetchAsBytes(fastaUrl1_16375333_16375833 as string),
-  "1:16376162-16376662": await fetchAsBytes(fastaUrl1_16376162_16376662 as string),
-  "1:17348965-17349469": await fetchAsBytes(fastaUrl1_17348965_17349469 as string),
-  "1:17348969-17349469": await fetchAsBytes(fastaUrl1_17348969_17349469 as string),
-  "1:17354844-17355344": await fetchAsBytes(fastaUrl1_17354844_17355344 as string),
-  "1:152520538-152521038": await fetchAsBytes(fastaUrl1_152520538_152521038 as string),
-  "2:47635417-47635917": await fetchAsBytes(fastaUrl2_47635417_47635917 as string),
-  "4:106320044-106320544": await fetchAsBytes(fastaUrl4_106320044_106320544 as string),
-  "7:42017061-42017561": await fetchAsBytes(fastaUrl7_42017061_42017561 as string),
-  "7:42064707-42065207": await fetchAsBytes(fastaUrl7_42064707_42065207 as string),
-  "8:61764893-61765393": await fetchAsBytes(fastaUrl8_61764893_61765393 as string),
-  "8:145140250-145140750": await fetchAsBytes(fastaUrl8_145140250_145140750 as string),
-  "9:107546383-107546883": await fetchAsBytes(fastaUrl9_107546383_107546883 as string),
-  "9:107584614-107585114": await fetchAsBytes(fastaUrl9_107584614_107585114 as string),
-  "10:126091249-126091749": await fetchAsBytes(fastaUrl10_126091249_126091749 as string),
-  "11:134013975-134014475": await fetchAsBytes(fastaUrl11_134013975_134014475 as string),
-  "13:77569878-77570378": await fetchAsBytes(fastaUrl13_77569878_77570378 as string),
-  "14:89307588-89308088": await fetchAsBytes(fastaUrl14_89307588_89308088 as string),
-  "14:89309945-89310445": await fetchAsBytes(fastaUrl14_89309945_89310445 as string),
-  "14:89336157-89336657": await fetchAsBytes(fastaUrl14_89336157_89336657 as string),
-  "14:105167610-105168110": await fetchAsBytes(fastaUrl14_105167610_105168110 as string),
-  "17:29555814-29556314": await fetchAsBytes(fastaUrl17_29555814_29556314 as string),
-  "17:29585172-29585672": await fetchAsBytes(fastaUrl17_29585172_29585672 as string),
-  "17:29663629-29664129": await fetchAsBytes(fastaUrl17_29663629_29664129 as string),
-  "17:29675976-29676476": await fetchAsBytes(fastaUrl17_29675976_29676476 as string),
-  "17:29683733-29684233": await fetchAsBytes(fastaUrl17_29683733_29684233 as string),
-  "19:11215896-11216396": await fetchAsBytes(fastaUrl19_11215896_11216396 as string),
-  "19:11223801-11224301": await fetchAsBytes(fastaUrl19_11223801_11224301 as string),
-  "19:17449149-17449649": await fetchAsBytes(fastaUrl19_17449149_17449649 as string),
-  "19:17451747-17452247": await fetchAsBytes(fastaUrl19_17451747_17452247 as string),
-  "20:62326742-62327242": await fetchAsBytes(fastaUrl20_62326742_62327242 as string),
-  "22:50627343-50627843": await fetchAsBytes(fastaUrl22_50627343_50627843 as string),
-  "22:50721296-50721796": await fetchAsBytes(fastaUrl22_50721296_50721796 as string),
-  "X:48932771-48933271": await fetchAsBytes(fastaUrlX_48932771_48933271 as string),
-  "Y:2655391-2655891": await fetchAsBytes(fastaUrlY_2655391_2655891 as string),
-  "MT:15076-15576": await fetchAsBytes(fastaUrlMT_15076_15576 as string),
-};
+export async function fetchCram() {
+  return await fetchAsBytes(cramUrl as string);
+}
 
-export const genesGz = await fetchAsBytes(genesUrl as string);
+export async function fetchCrai() {
+  return await fetchAsBytes(craiUrl as string);
+}
 
-export const vcfMeta = vcfMetaJson as unknown as Metadata;
+export const decisionTree = decisionTreeJson as unknown as DecisionTree;
 
-export const vcfFamily = await fetchAsBytes(vcfUrlFamily as string);
+export const sampleTree = sampleTreeJson as unknown as DecisionTree;
 
-export const vcfNoVep = await fetchAsBytes(vcfUrlNoVep as string);
+export async function fetchFastaGz() {
+  return {
+    "1:10042288-10042788": await fetchAsBytes(fastaUrl1_10042288_10042788 as string),
+    "1:16375333-16375833": await fetchAsBytes(fastaUrl1_16375333_16375833 as string),
+    "1:16376162-16376662": await fetchAsBytes(fastaUrl1_16376162_16376662 as string),
+    "1:17348965-17349469": await fetchAsBytes(fastaUrl1_17348965_17349469 as string),
+    "1:17348969-17349469": await fetchAsBytes(fastaUrl1_17348969_17349469 as string),
+    "1:17354844-17355344": await fetchAsBytes(fastaUrl1_17354844_17355344 as string),
+    "1:152520538-152521038": await fetchAsBytes(fastaUrl1_152520538_152521038 as string),
+    "2:47635417-47635917": await fetchAsBytes(fastaUrl2_47635417_47635917 as string),
+    "4:106320044-106320544": await fetchAsBytes(fastaUrl4_106320044_106320544 as string),
+    "7:42017061-42017561": await fetchAsBytes(fastaUrl7_42017061_42017561 as string),
+    "7:42064707-42065207": await fetchAsBytes(fastaUrl7_42064707_42065207 as string),
+    "8:61764893-61765393": await fetchAsBytes(fastaUrl8_61764893_61765393 as string),
+    "8:145140250-145140750": await fetchAsBytes(fastaUrl8_145140250_145140750 as string),
+    "9:107546383-107546883": await fetchAsBytes(fastaUrl9_107546383_107546883 as string),
+    "9:107584614-107585114": await fetchAsBytes(fastaUrl9_107584614_107585114 as string),
+    "10:126091249-126091749": await fetchAsBytes(fastaUrl10_126091249_126091749 as string),
+    "11:134013975-134014475": await fetchAsBytes(fastaUrl11_134013975_134014475 as string),
+    "13:77569878-77570378": await fetchAsBytes(fastaUrl13_77569878_77570378 as string),
+    "14:89307588-89308088": await fetchAsBytes(fastaUrl14_89307588_89308088 as string),
+    "14:89309945-89310445": await fetchAsBytes(fastaUrl14_89309945_89310445 as string),
+    "14:89336157-89336657": await fetchAsBytes(fastaUrl14_89336157_89336657 as string),
+    "14:105167610-105168110": await fetchAsBytes(fastaUrl14_105167610_105168110 as string),
+    "17:29555814-29556314": await fetchAsBytes(fastaUrl17_29555814_29556314 as string),
+    "17:29585172-29585672": await fetchAsBytes(fastaUrl17_29585172_29585672 as string),
+    "17:29663629-29664129": await fetchAsBytes(fastaUrl17_29663629_29664129 as string),
+    "17:29675976-29676476": await fetchAsBytes(fastaUrl17_29675976_29676476 as string),
+    "17:29683733-29684233": await fetchAsBytes(fastaUrl17_29683733_29684233 as string),
+    "19:11215896-11216396": await fetchAsBytes(fastaUrl19_11215896_11216396 as string),
+    "19:11223801-11224301": await fetchAsBytes(fastaUrl19_11223801_11224301 as string),
+    "19:17449149-17449649": await fetchAsBytes(fastaUrl19_17449149_17449649 as string),
+    "19:17451747-17452247": await fetchAsBytes(fastaUrl19_17451747_17452247 as string),
+    "20:62326742-62327242": await fetchAsBytes(fastaUrl20_62326742_62327242 as string),
+    "22:50627343-50627843": await fetchAsBytes(fastaUrl22_50627343_50627843 as string),
+    "22:50721296-50721796": await fetchAsBytes(fastaUrl22_50721296_50721796 as string),
+    "X:48932771-48933271": await fetchAsBytes(fastaUrlX_48932771_48933271 as string),
+    "Y:2655391-2655891": await fetchAsBytes(fastaUrlY_2655391_2655891 as string),
+    "MT:15076-15576": await fetchAsBytes(fastaUrlMT_15076_15576 as string),
+  };
+}
 
-export const vcfSamples0 = await fetchAsBytes(vcfUrlSamples0 as string);
+export async function fetchGenesGz() {
+  return await fetchAsBytes(genesUrl as string);
+}
 
-export const vcfSamples1 = await fetchAsBytes(vcfUrlSamples1 as string);
+export const vcfMeta = vcfMetaJson as unknown as SupplementaryMetadata;
 
-export const vcfSamples100 = await fetchAsBytes(vcfUrlSamples100 as string);
+export async function fetchVcfFamily() {
+  return await fetchAsBytes(vcfUrlFamily as string);
+}
 
 export const samplesFamily = {
   samples: [
@@ -183,77 +187,3 @@ export const samplesFamily = {
     },
   ],
 };
-export const samplesFamilyDuoPlusSister = {
-  samples: [
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "Patient",
-        paternalId: "Father",
-        maternalId: "0",
-        sex: "MALE",
-        affectedStatus: "AFFECTED",
-      },
-      index: 0,
-      proband: true,
-    },
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "Sister",
-        paternalId: "0",
-        maternalId: "0",
-        sex: "FEMALE",
-        affectedStatus: "UNAFFECTED",
-      },
-      index: 3,
-      proband: false,
-    },
-    {
-      person: {
-        familyId: "FAM001",
-        individualId: "Father",
-        paternalId: "0",
-        maternalId: "0",
-        sex: "MALE",
-        affectedStatus: "UNAFFECTED",
-      },
-      index: 1,
-      proband: false,
-    },
-  ],
-  phenotypes: [
-    {
-      phenotypicFeaturesList: [
-        {
-          type: {
-            id: "HP:0000951",
-            label: "HP:0000951",
-          },
-        },
-        {
-          type: {
-            id: "HP:0003124",
-            label: "HP:0003124",
-          },
-        },
-      ],
-      subject: {
-        id: "Patient",
-      },
-    },
-    {
-      phenotypicFeaturesList: [
-        {
-          type: {
-            id: "HP:0000951",
-            label: "HP:0000951",
-          },
-        },
-      ],
-      subject: {
-        id: "Sister",
-      },
-    },
-  ],
-};